Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife

Transcriptomic plasticity in brown adipose tissue contributes to an enhanced capacity for nonshivering thermogenesis in deer mice

(2016) Jonathan P. Velotta et al.   MOLECULAR ECOLOGY

Trade-offs in osmoregulation and parallel shifts in molecular function follow ecological transitions to freshwater in the Alewife

(2015) Jonathan P. Velotta et al.   EVOLUTION

Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus

(2015) R. S. Brennan et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

A new model for fish ion regulation: identification of ionocytes in freshwater- and seawater-acclimated medaka (Oryzias latipes)

(2014) Hao-Hsuan Hsu et al.   CELL AND TISSUE RESEARCH

Beta-thymosin gene polymorphism associated with freshwater invasiveness of alewife (Alosa pseudoharengus)

(2014) Katarzyna Michalak et al.   Journal of Experimental Zoology Part A-Ecological Genetics and Physiology

Origins and functional diversification of salinity-responsive Na+, K+ATPase α1 paralogs in salmonids

(2014) Anne C. Dalziel et al.   MOLECULAR ECOLOGY

Relaxed selection causes microevolution of seawater osmoregulation and gene expression in landlocked Alewives

(2014) Jonathan P. Velotta et al.   OECOLOGIA

Small Changes in Gene Expression of Targeted Osmoregulatory Genes When Exposing Marine and Freshwater Threespine Stickleback (Gasterosteus aculeatus) to Abrupt Salinity Transfers

(2014) Annette Taugbøl et al.   PLoS One

FUNCTIONAL GENOMICS OF ADAPTATION TO HYPOXIC COLD-STRESS IN HIGH-ALTITUDE DEER MICE: TRANSCRIPTOMIC PLASTICITY AND THERMOGENIC PERFORMANCE

(2013) Zachary A. Cheviron et al.   EVOLUTION

FUNCTIONAL AND POPULATION GENOMIC DIVERGENCE WITHIN AND BETWEEN TWO SPECIES OF KILLIFISH ADAPTED TO DIFFERENT OSMOTIC NICHES

(2013) Genevieve M. Kozak et al.   EVOLUTION

Local adaptation to salinity in the three-spined stickleback?

(2013) J. DeFaveri et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Differential regulation of sodium-potassium pump isoforms during smolt development and seawater exposure of Atlantic salmon

(2013) S. D. McCormick et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Differential expression of Na+, K+-ATPase α-1 isoforms during seawater acclimation in the amphidromous galaxiid fish Galaxias maculatus

(2012) Mauricio A. Urbina et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

Branchial ionocyte organization and ion-transport protein expression in juvenile alewives acclimated to freshwater or seawater

(2012) A. K. Christensen et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

(2012) A. Whitehead   JOURNAL OF EXPERIMENTAL BIOLOGY

Salinity- and population-dependent genome regulatory response during osmotic acclimation in the killifish (Fundulus heteroclitus) gill

(2012) A. Whitehead et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

The Combinatorial Nature of Osmosensing in Fishes

(2012) Dietmar Kültz   PHYSIOLOGY

Genetic Divergence between Freshwater and Marine Morphs of Alewife (Alosa pseudoharengus): A ‘Next-Generation’ Sequencing Analysis

(2012) Sergiusz Czesny et al.   PLoS One

New insights into gill ionocyte and ion transporter function in euryhaline and diadromous fish

(2012) Junya Hiroi et al.   RESPIRATORY PHYSIOLOGY & NEUROBIOLOGY

GLOBAL ANALYSIS OF GENES INVOLVED IN FRESHWATER ADAPTATION IN THREESPINE STICKLEBACKS (GASTEROSTEUS ACULEATUS)

(2011) Jacquelin DeFaveri et al.   EVOLUTION

PUMPING IONS: RAPID PARALLEL EVOLUTION OF IONIC REGULATION FOLLOWING HABITAT INVASIONS

(2011) Carol Eunmi Lee et al.   EVOLUTION

Switching of Na+, K+-ATPase isoforms by salinity and prolactin in the gill of a cichlid fish

(2011) C K Tipsmark et al.   JOURNAL OF ENDOCRINOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genomic mechanisms of evolved physiological plasticity in killifish distributed along an environmental salinity gradient

(2011) A. Whitehead et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Co-ordination of osmotic stress responses through osmosensing and signal transduction events in fishes

(2010) T. G. Evans   JOURNAL OF FISH BIOLOGY

A High Incidence of Selection on Physiologically Important Genes in the Three-Spined Stickleback, Gasterosteus aculeatus

(2010) Y. Shimada et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Mechanism of development of ionocytes rich in vacuolar-type H+-ATPase in the skin of zebrafish larvae

(2009) Masahiro Esaki et al.   DEVELOPMENTAL BIOLOGY

ADAPTIVE DIVERGENCE BETWEEN FRESHWATER AND MARINE STICKLEBACKS: INSIGHTS INTO THE ROLE OF PHENOTYPIC PLASTICITY FROM AN INTEGRATED ANALYSIS OF CANDIDATE GENE EXPRESSION

(2009) R. J. Scott McCairns et al.   EVOLUTION

Distinct freshwater and seawater isoforms of Na+/K+-ATPase in gill chloride cells of Atlantic salmon

(2009) S. D. McCormick et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Re-evaluating the costs and limits of adaptive phenotypic plasticity

(2009) J. R. Auld et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Relaxed selection in the wild

(2009) David C. Lahti et al.   TRENDS IN ECOLOGY & EVOLUTION

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Salinity regulates claudin mRNA and protein expression in the teleost gill

(2008) Christian K. Tipsmark et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Teleost fish osmoregulation: what have we learned since August Krogh, Homer Smith, and Ancel Keys

(2008) David H. Evans   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Interpopulation differences in expression of candidate genes for salinity tolerance in winter migrating anadromous brown trout (Salmo trutta L.)

(2008) Peter F Larsen et al.   BMC GENETICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Multiplicity of expression of Na+,K+-ATPase  -subunit isoforms in the gill of Atlantic salmon (Salmo salar): cellular localisation and absolute quantification in response to salinity change

(2008) S. S. Madsen et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Evidence for an apical Na-Cl cotransporter involved in ion uptake in a teleost fish

(2008) J. Hiroi et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Importance for Absorption of Na+ from Freshwater of Lysine, Valine and Serine Substitutions in the α1a-Isoform of Na,K-ATPase in the Gills of Rainbow Trout (Oncorhynchus mykiss) and Atlantic Salmon (Salmo salar)

(2008) Peter Leth Jorgensen   JOURNAL OF MEMBRANE BIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS